The constancy of global regulation across a species: the concentrations of ppGpp and RpoS are strain-specific in Escherichia coli

Background: Sigma factors and the alarmone ppGpp control the allocation of RNA polymerase to promoters under stressful conditions. Both ppGpp and the sigma factor sigma(S) (RpoS) are potentially subject to variability across the species Escherichia coli. To find out the extent of strain variation we measured the level of RpoS and ppGpp using 31 E. coli strains from the ECOR collection and one reference K-12 strain. Results: Nine ECORs had highly deleterious mutations in rpoS, 12 had RpoS protein up to 7-fold above that of the reference strain MG1655 and the remainder had comparable or lower levels. Strain variation was also evident in ppGpp accumulation under carbon starvation and spoT mutations were present in several low-ppGpp strains. Three relationships between RpoS and ppGpp levels were found: isolates with zero RpoS but various ppGpp levels, strains where RpoS levels were proportional to ppGpp and a third unexpected class in which RpoS was present but not proportional to ppGpp concentration. High-RpoS and high-ppGpp strains accumulated rpoS mutations under nutrient limitation, providing a source of polymorphisms. Conclusions: The ppGpp and sigma(S) variance means that the expression of genes involved in translation, stress and other traits affected by ppGpp and/or RpoS are likely to be strain-specific and suggest that influential components of regulatory networks are frequently reset by microevolution. Different strains of E. coli have different relationships between ppGpp and RpoS levels and only some exhibit a proportionality between increasing ppGpp and RpoS levels as demonstrated for E. coli K-12.

Rapid formation of isoprene photo-oxidation products observed in Amazonia

Isoprene represents the single most important reactive hydrocarbon for atmospheric chemistry in the tropical atmosphere. It plays a central role in global and regional atmospheric chemistry and possible climate feedbacks. Photo-oxidation of primary hydrocarbons (e. g. isoprene) leads to the formation of oxygenated VOCs (OVOCs). The evolution of these intermediates affects the oxidative capacity of the atmosphere (by reacting with OH) and can contribute to secondary aerosol formation, a poorly understood process. An accurate and quantitative understanding of VOC oxidation processes is needed for model simulations of regional air quality and global climate. Based on field measurements conducted during the Amazonian Aerosol Characterization Experiment (AMAZE-08) we show that the production of certain OVOCs (e. g. hydroxyacetone) from isoprene photo-oxidation in the lower atmosphere is significantly underpredicted by standard chemistry schemes. Recently reported fast secondary production could explain 50% of the observed discrepancy with the remaining part possibly produced via a novel primary production channel, which has been proposed theoretically. The observations of OVOCs are also used to test a recently proposed HO(x) recycling mechanism via degradation of isoprene peroxy radicals. If generalized our observations suggest that prompt photochemical formation of OVOCs and other uncertainties in VOC oxidation schemes could result in uncertainties of modelled OH reactivity, potentially explaining a fraction of the missing OH sink over forests which has previously been largely attributed to a missing source of primary biogenic VOCs.

Angular-planar CMB power spectrum

Gaussianity and statistical isotropy of the Universe are modern cosmology's minimal set of hypotheses. In this work we introduce a new statistical test to detect observational deviations from this minimal set. By defining the temperature correlation function over the whole celestial sphere, we are able to independently quantify both angular and planar dependence (modulations) of the CMB temperature power spectrum over different slices of this sphere. Given that planar dependence leads to further modulations of the usual angular power spectrum C(l), this test can potentially reveal richer structures in the morphology of the primordial temperature field. We have also constructed an unbiased estimator for this angular-planar power spectrum which naturally generalizes the estimator for the usual C(l)'s. With the help of a chi-square analysis, we have used this estimator to search for observational deviations of statistical isotropy in WMAP's 5 year release data set (ILC5), where we found only slight anomalies on the angular scales l = 7 and l = 8. Since this angular-planar statistic is model-independent, it is ideal to employ in searches of statistical anisotropy (e.g., contaminations from the galactic plane) and to characterize non-Gaussianities.

Quantum fields with noncommutative target spaces

Quantum field theories (QFT's) on noncommutative spacetimes are currently under intensive study. Usually such theories have world sheet noncommutativity. In the present work, instead, we study QFT's with commutative world sheet and noncommutative target space. Such noncommutativity can be interpreted in terms of twisted statistics and is related to earlier work of Oeckl [R. Oeckl, Commun. Math. Phys. 217, 451 (2001)], and others [A. P. Balachandran, G. Mangano, A. Pinzul, and S. Vaidya, Int. J. Mod. Phys. A 21, 3111 (2006); A. P. Balachandran, A. Pinzul, and B. A. Qureshi, Phys. Lett. B 634,434 (2006); A.P. Balachandran, A. Pinzul, B.A. Qureshi, and S. Vaidya, arXiv:hep-th/0608138; A.P. Balachandran, T. R. Govindarajan, G. Mangano, A. Pinzul, B.A. Qureshi, and S. Vaidya, Phys. Rev. D 75, 045009 (2007); A. Pinzul, Int. J. Mod. Phys. A 20, 6268 (2005); G. Fiore and J. Wess, Phys. Rev. D 75, 105022 (2007); Y. Sasai and N. Sasakura, Prog. Theor. Phys. 118, 785 (2007)]. The twisted spectra of their free Hamiltonians has been found earlier by Carmona et al. [J. M. Carmona, J. L. Cortes, J. Gamboa, and F. Mendez, Phys. Lett. B 565, 222 (2003); J. M. Carmona, J. L. Cortes, J. Gamboa, and F. Mendez, J. High Energy Phys. 03 (2003) 058]. We review their derivation and then compute the partition function of one such typical theory. It leads to a deformed blackbody spectrum, which is analyzed in detail. The difference between the usual and the deformed blackbody spectrum appears in the region of high frequencies. Therefore we expect that the deformed blackbody radiation may potentially be used to compute a Greisen-Zatsepin-Kuzmin cutoff which will depend on the noncommutative parameter theta.

Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Late Entry into HIV Care: Estimated Impact on AIDS Mortality Rates in Brazil, 2003-2006

Background: Worldwide, a high proportion of HIV-infected individuals enter into HIV care late. Here, our objective was to estimate the impact that late entry into HIV care has had on AIDS mortality rates in Brazil. Methodology/Principal Findings: We analyzed data from information systems regarding HIV-infected adults who sought treatment at public health care facilities in Brazil from 2003 to 2006. We initially estimated the prevalence of late entry into HIV care, as well as the probability of death in the first 12 months, the percentage of the risk of death attributable to late entry, and the number of avoidable deaths. We subsequently adjusted the annual AIDS mortality rate by excluding such deaths. Of the 115,369 patients evaluated, 50,358 (43.6%) had entered HIV care late, and 18,002 died in the first 12 months, representing a 16.5% probability of death in the first 12 months (95% CI: 16.3-16.7). By comparing patients who entered HIV care late with those who gained timely access, we found that the risk ratio for death was 49.5 (95% CI: 45.1-54.2). The percentage of the risk of death attributable to late entry was 95.5%, translating to 17,189 potentially avoidable deaths. Averting those deaths would have lowered the 2003-2006 AIDS mortality rate by 39.5%. Including asymptomatic patients with CD4(+) T cell counts >200 and <= 350 cells/mm(3) in the group who entered HIV care late increased this proportion by 1.8%. Conclusions/Significance: In Brazil, antiretroviral drugs reduced AIDS mortality by 43%. Timely entry would reduce that rate by a similar proportion, as well as resulting in a 45.2% increase in the effectiveness of the program for HIV care. The World Health Organization recommendation that asymptomatic patients with CD4(+) T cell counts <= 350 cells/mm(3) be treated would not have a significant impact on this scenario.

Genome-Wide Detection of Serpentine Receptor-Like Proteins in Malaria Parasites

Serpentine receptors comprise a large family of membrane receptors distributed over diverse organisms, such as bacteria, fungi, plants and all metazoans. However, the presence of serpentine receptors in protozoan parasites is largely unknown so far. In the present study we performed a genome-wide search for proteins containing seven transmembrane domains (7TM) in the human malaria parasite Plasmodium falciparum and identified four serpentine receptor-like proteins. These proteins, denoted PfSR1, PfSR10, PfSR12 and PfSR25, show membrane topologies that resemble those exhibited by members belonging to different families of serpentine receptors. Expression of the pfsrs genes was detected by Real Time PCR in P. falciparum intraerythrocytic stages, indicating that they potentially code for functional proteins. We also found corresponding homologues for the PfSRs in five other Plasmodium species, two primate and three rodent parasites. PfSR10 and 25 are the most conserved receptors among the different species, while PfSR1 and 12 are more divergent. Interestingly, we found that PfSR10 and PfSR12 possess similarity to orphan serpentine receptors of other organisms. The identification of potential parasite membrane receptors raises a new perspective for essential aspects of malaria parasite host cell infection.

Conversion to soy on the Amazonian agricultural frontier increases streamflow without affecting stormflow dynamics

Large-scale soy agriculture in the southern Brazilian Amazon now rivals deforestation for pasture as the region`s predominant form of land use change. Such landscape-level change can have substantial consequences for local and regional hydrology, but these effects remain relatively unstudied in this ecologically and economically important region. We examined how the conversion to soy agriculture influences water balances and stormflows using stream discharge (water yields) and the timing of discharge (stream hydrographs) in small (2.5-13.5 km2) forested and soy headwater watersheds in the Upper Xingu Watershed in the state of Mato Grosso, Brazil. We monitored water yield for 1 year in three forested and four soy watersheds. Mean daily water yields were approximately four times higher in soy than forested watersheds, and soy watersheds showed greater seasonal variability in discharge. The contribution of stormflows to annual streamflow in all streams was low (< 13% of annual streamflow), and the contribution of stormflow to streamflow did not differ between land uses. If the increases in water yield observed in this study are typical, landscape-scale conversion to soy substantially alters water-balance, potentially altering the regional hydrology over large areas of the southern Amazon.

Greenhouse gas emissions from alternative futures of deforestation and agricultural management in the southern Amazon

The Brazilian Amazon is one of the most rapidly developing agricultural areas in the world and represents a potentially large future source of greenhouse gases from land clearing and subsequent agricultural management. In an integrated approach, we estimate the greenhouse gas dynamics of natural ecosystems and agricultural ecosystems after clearing in the context of a future climate. We examine scenarios of deforestation and postclearing land use to estimate the future (2006-2050) impacts on carbon dioxide (CO(2)), methane (CH(4)), and nitrous oxide (N(2)O) emissions from the agricultural frontier state of Mato Grosso, using a process-based biogeochemistry model, the Terrestrial Ecosystems Model (TEM). We estimate a net emission of greenhouse gases from Mato Grosso, ranging from 2.8 to 15.9 Pg CO(2)-equivalents (CO(2)-e) from 2006 to 2050. Deforestation is the largest source of greenhouse gas emissions over this period, but land uses following clearing account for a substantial portion (24-49%) of the net greenhouse gas budget. Due to land-cover and land-use change, there is a small foregone carbon sequestration of 0.2-0.4 Pg CO(2)-e by natural forests and cerrado between 2006 and 2050. Both deforestation and future land-use management play important roles in the net greenhouse gas emissions of this frontier, suggesting that both should be considered in emissions policies. We find that avoided deforestation remains the best strategy for minimizing future greenhouse gas emissions from Mato Grosso.

Do plant species influence soil CO(2) and N(2)O fluxes in a diverse tropical forest?

To test whether plant species influence greenhouse gas production in diverse ecosystems, we measured wet season soil CO(2) and N(2)O fluxes close to similar to 300 large (>35 cm in diameter at breast height (DBH)) trees of 15 species at three clay-rich forest sites in central Amazonia. We found that soil CO(2) fluxes were 38% higher near large trees than at control sites >10 m away from any tree (P < 0.0001). After adjusting for large tree presence, a multiple linear regression of soil temperature, bulk density, and liana DBH explained 19% of remaining CO(2) flux variability. Soil N(2)O fluxes adjacent to Caryocar villosum, Lecythis lurida, Schefflera morototoni, and Manilkara huberi were 84%-196% greater than Erisma uncinatum and Vochysia maxima, both Vochysiaceae. Tree species identity was the most important explanatory factor for N(2)O fluxes, accounting for more than twice the N(2)O flux variability as all other factors combined. Two observations suggest a mechanism for this finding: (1) sugar addition increased N(2)O fluxes near C. villosum twice as much (P < 0.05) as near Vochysiaceae and (2) species mean N(2)O fluxes were strongly negatively correlated with tree growth rate (P = 0.002). These observations imply that through enhanced belowground carbon allocation liana and tree species can stimulate soil CO(2) and N(2)O fluxes (by enhancing denitrification when carbon limits microbial metabolism). Alternatively, low N(2)O fluxes potentially result from strong competition of tree species with microbes for nutrients. Species-specific patterns in CO(2) and N(2)O fluxes demonstrate that plant species can influence soil biogeochemical processes in a diverse tropical forest.

DISTRIBUTION OF CAPYBARAS IN AN AGROECOSYSTEM, SOUTHEASTERN BRAZIL, BASED ON ECOLOGICAL NICHE MODELING

Southeastern Brazil has seen dramatic landscape modifications in recent decades, due to expansion of agriculture and urban areas; these changes have influenced the distribution and abundance of vertebrates. We developed predictive models of ecological and spatial distributions of capybaras (Hydrochoerus hydrochaeris) using ecological niche modeling. Most Occurrences of capybaras were in flat areas with water bodies Surrounded by sugarcane and pasture. More than 75% of the Piracicaba River basin was estimated as potentially habitable by capybara. The models had low omission error (2.3-3.4%), but higher commission error (91.0-98.5%); these ""model failures"" seem to be more related to local habitat characteristics than to spatial ones. The potential distribution of capybaras in the basin is associated with anthropogenic habitats, particularly with intensive land use for agriculture.

Dynamics of carbon, biomass, and structure in two Amazonian forests

Amazon forests are potentially globally significant sources or sinks for atmospheric carbon dioxide. In this study, we characterize the spatial trends in carbon storage and fluxes in both live and dead biomass (necromass) in two Amazonian forests, the Biological Dynamic of Forest Fragments Project (BDFFP), near Manaus, Amazonas, and the Tapajos National Forest (TNF) near Santarem, Para. We assessed coarse woody debris (CWD) stocks, tree growth, mortality, and recruitment in ground-based plots distributed across the terra firme forest at both sites. Carbon dynamics were similar within each site, but differed significantly between the sites. The BDFFP and the TNF held comparable live biomass (167 +/- 7.6 MgC.ha(-1) versus 149 +/- 6.0 MgC.ha(-1), respectively), but stocks of CWD were 2.5 times larger at TNF (16.2 +/- 1.5 MgC.ha(-1) at BDFFP, versus 40.1 +/- 3.9 MgC.ha(-1) at TNF). A model of current forest dynamics suggests that the BDFFP was close to carbon balance, and its size class structure approximated a steady state. The TNF, by contrast, showed rapid carbon accrual to live biomass (3.24 +/- 0.22 MgC.ha(-1).a(-1) in TNF, 2.59 +/- 0.16 MgC.ha(-1).a(-1) in BDFFP), which was more than offset by losses from large stocks of CWD, as well as ongoing shifts of biomass among size classes. This pattern in the TNF suggests recovery from a significant disturbance. The net loss of carbon from the TNF will likely last 10 - 15 years after the initial disturbance (controlled by the rate of decay of coarse woody debris), followed by uptake of carbon as the forest size class structure and composition continue to shift. The frequency and longevity of forests showing such disequilibruim dynamics within the larger matrix of the Amazon remains an essential question to understanding Amazonian carbon balance.

Small rivers in the southwestern Amazon and their role in CO(2) outgassing

A recent estimate of CO(2) outgassing from Amazonian wetlands suggests that an order of magnitude more CO(2) leaves rivers through gas exchange with the atmosphere than is exported to the ocean as organic plus inorganic carbon. However, the contribution of smaller rivers is still poorly understood, mainly because of limitations in mapping their spatial extent. Considering that the largest extension of the Amazon River network is composed of small rivers, the authors` objective was to elucidate their role in air-water CO(2) exchange by developing a geographic information system ( GIS)- based model to calculate the surface area covered by rivers with channels less than 100 m wide, combined with estimated CO(2) outgassing rates at the Ji-Parana River basin, in the western Amazon. Estimated CO(2) outgassing was the main carbon export pathway for this river basin, totaling 289 Gg C yr(-1), about 2.4 times the amount of carbon exported as dissolved inorganic carbon ( 121 Gg C yr(-1)) and 1.6 times the dissolved organic carbon export ( 185 Gg C yr(-1)). The relationships established here between drainage area and channel width provide a new model for determining small river surface area, allowing regional extrapolations of air - water gas exchange. Applying this model to the entire Amazon River network of channels less than 100 m wide ( third to fifth order), the authors calculate that the surface area of small rivers is 0.3 +/- 0.05 million km(2), and it is potentially evading to the atmosphere 170 +/- 42 Tg C yr(-1) as CO(2). Therefore, these ecosystems play an important role in the regional carbon balance.

Arsenic and Chromium in Brazilian Agricultural Supplies

Arsenic (As) and chromium (Cr) contents were measured in agricultural supplies used at different farms in Sao Paulo State, Brazil. The highest mass fractions of As were found in thermophosphates, reaching levels of 4 mg/kg. The highest mass fractions of Cr (21 g/kg) were found in calcium magnesium silicate, while the thermophosphates also presented high values reaching approximately 1 g/kg. The levels of As were within Brazilian guidelines, but the values of Cr in thermophosphates exceeded the levels permitted in Brazil. The As content in fertilizers may be considered safe (5 mg/kg) in terms of environmental pollution. However, the Cr content in calcium magnesium silicate following continuous use may constitute a significant problem in Brazil due to potentially increasing levels of this metal in soils.

Preliminary studies of laser-induced breakdown spectrometry for the determination of Ba, Cd, Cr and Pb in toys

The performance of laser-induced breakdown spectrometry (LIBS) for the determination of Ba, Cd, Cr and Pb in toys has been evaluated by using a Nd:YAG laser operating at 1064 nm and an Echelle spectrometer with intensified charge-coupled device detector. Samples were purchased in different cities of Sao Paulo State market and analyzed directly without sample preparation. Laser-induced breakdown spectrometry experimental conditions (number of pulses, delay time. integration time gate and pulse energy) were optimized by using a Doehlert design. Laser-induced breakdown spectrometry signals correlated reasonably well with inductively coupled plasma optical emission spectrometry (ICP OES) concentrations after microwave-assisted acid digestion of selected samples. Thermal analysis was used for polymer identification and scanning electron microscopy to Visualize differences in crater geometry of different polymers employed for toy fabrication. Results indicate that laser-induced breakdown spectrometry can be proposed as a rapid screening method for investigation of potentially toxic elements in toys. The unique application of laser-induced breakdown spectrometry for identification of contaminants in successive layers of ink and polymer is also demonstrated. (C) 2009 Elsevier B.V. All rights reserved.